The primary aim of this research was to study the effectiveness of various strains of antagonist microorganisms and biological preparations against Meloidogyne hapla, in addition to their impact on the quality of tomato fruits and crop structure. Four microorganism strains and three registered environmentally safe nematicides were used in the experiment presented herein. The results showed that the strains Paecilomyces lilacinus F-22BK/6 and Arthrobotrys conoides F-22BK/4 had the greatest biological efficacy, reducing the number of galls on tomato plants by 91.8% and 88.4%, values comparable with the results of the chemical control Vydate 5G. The Metarhizium anisopliae F-22BK/2 and Arthrobotrys conoides F-22BK/4 treatments showed the best results, increasing the fruit weight by 8.6% and 9.9%, in addition to increasing the tomato yield by 5.0% and 13.3%. These strains contributed to an increase in sugar content, whereas the concentration of vitamin C was reduced in the Trichoderma viride F-294 and Fitoverm treatments, indicating a high level of oxidative stress in the latter treatments. The results of this study confirm the prospects of using biological nematicides against phytoparasitic nematodes, which will not only enable effective control of their population but also improve the quality of agricultural products, minimizing harm to the environment and human health.